Crystal structure of the N-terminal RRM of the U2AF large subunit

Experimental Data Snapshot

  • Resolution: 1.47 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.137 

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Alternative Conformations at the RNA-binding Surface of the N-terminal U2AF(65) RNA Recognition Motif.

Thickman, K.R.Sickmier, E.A.Kielkopf, C.L.

(2007) J Mol Biol 366: 703-710

  • DOI: https://doi.org/10.1016/j.jmb.2006.11.077
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The essential pre-mRNA splicing factor, U2 auxiliary factor 65KD (U2AF(65)) recognizes the polypyrimidine tract (Py-tract) consensus sequence of the pre-mRNA using two RNA recognition motifs (RRMs), the most prevalent class of eukaryotic RNA-binding domain. The Py-tracts of higher eukaryotic pre-mRNAs are often interrupted with purines, yet U2AF(65) must identify these degenerate Py-tracts for accurate pre-mRNA splicing. Previously, the structure of a U2AF(65) variant in complex with poly(U) RNA suggested that rearrangement of flexible side-chains or bound water molecules may contribute to degenerate Py-tract recognition by U2AF(65). Here, the X-ray structure of the N-terminal RRM domain of U2AF(65) (RRM1) is described at 1.47 A resolution in the absence of RNA. Notably, RNA-binding by U2AF(65) selectively stabilizes pre-existing alternative conformations of three side-chains located at the RNA interface (Arg150, Lys225, and Arg227). Additionally, a flexible loop connecting the beta2/beta3 strands undergoes a conformational change to interact with the RNA. These pre-existing alternative conformations may contribute to the ability of U2AF(65) to recognize a variety of Py-tract sequences. This rare, high-resolution view of an important member of the RRM class of RNA-binding domains highlights the role of alternative side-chain conformations in RNA recognition.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor U2AF 65 kDa subunit87Homo sapiensMutation(s): 0 
Gene Names: U2AF2U2AF65
UniProt & NIH Common Fund Data Resources
Find proteins for P26368 (Homo sapiens)
Explore P26368 
Go to UniProtKB:  P26368
GTEx:  ENSG00000063244 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26368
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.47 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.137 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.07α = 90
b = 29.07β = 90
c = 184.71γ = 90
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
PROTEUM PLUSdata reduction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations